The nitrification process is highly feasible for treating high-ammonia nitrogen and low C/N ratio wastewater. By using thermal shock to treat embedded activated sludge, the accumulation of NO₂^--N has been successfully achieved. To study the changes in microbial communities within the embedded particles before and after heat shock, and to reveal their succession patterns and dominant flora, the present experiment was carried out to analyze the community structure of microorganisms in the three phases of pre-domestication, post-domestication, and post-heat-shock by using Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE), as well as to carry out species identification and phylogenetic analyses by the molecular cloning method. The 16S rDNA sequence analysis of the characteristic bands of the total bacterial DGGE spectrum showed that the activated sludge had the most species before domestication. As domestication proceeded, the total bacterial diversity decreased. In contrast, the species of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) increased significantly, and the nitrification performance of the sludge was enhanced. The thermal shock did not have a significant effect on the diversity of the AOB populations but had a great effect on the NOBs, and the dominant genera of the NOBs were almost completely inactivated.